Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium

Title: Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium. Aim: To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods: Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16S and 18S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results: In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion: Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turnaround time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.

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Descemet Membrane Endothelial Keratoplasty: NGS Metagenomics-Optimized Tissue Preparation and Surgical Technique. Summary of the Doctoral Thesis

10.25143/prom-rsu_2021-21_dts ◽

2021 ◽

Author(s):

◽

Davide Borroni ◽

Keyword(s):

Next Generation Sequencing ◽

Turnaround Time ◽

Storage Conditions ◽

Tissue Preparation ◽

Next Generation ◽

Human Donor ◽

Taxonomic Profiling ◽

Storage Media ◽

Hypothermic Storage ◽

Generation Sequencing

Title: Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium. Aim: To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods: Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16S and 18S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results: In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion: Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turnaround time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.

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Next-generation sequencing technologies and their application to the study and control of bacterial infections

Clinical Microbiology and Infection ◽

10.1016/j.cmi.2017.10.013 ◽

2018 ◽

Vol 24 (4) ◽

pp. 335-341 ◽

Cited By ~ 151

Author(s):

J. Besser ◽

H.A. Carleton ◽

P. Gerner-Smidt ◽

R.L. Lindsey ◽

E. Trees

Keyword(s):

Next Generation Sequencing ◽

Bacterial Infections ◽

Next Generation ◽

Sequencing Technologies ◽

And Control ◽

Generation Sequencing

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Genomic characterization of fecal microbial communities in severely sick humans and broiler chickens using next generation sequencing

10.21203/rs.2.22699/v1 ◽

2020 ◽

Author(s):

Ome Kalsoom Afridi ◽

Johar Ali ◽

Jeong Ho Chang

Keyword(s):

Next Generation Sequencing ◽

Microbial Communities ◽

Broiler Chickens ◽

Human Subjects ◽

Fecal Microbiota ◽

Next Generation ◽

Microbial Association ◽

Taxonomic Profiling ◽

Microbial Dysbiosis ◽

Generation Sequencing

Abstract Background: Microbiota plays an important role in food safety and its alteration poses a serious threat to humans. Comparative microbiome profiling using next-generation sequencing (NGS) enabled the understanding of microbial diversity and similarity between different species. In this study, we used NGS to profile the fecal microbiota of sick human and broiler chickens. A total of 26 fecal samples were collected from severely sick human subjects (n= 13) and broiler chickens (n=13) with similar symptoms. Results: The total number of microbial species detected in broiler chickens fecal microbiota was higher than that of humans. Phylum Proteobacteria was the most abundant in both human and broiler chickens fecal microbiota while Tenericutes was found to be least abundant in both species. Phylum Actinobacteria was found only in the human fecal microbiota. In both humans and broiler chickens, E.coli was found to be phylogenetically related suggesting a microbial association between both species. Conclusion: NGS based taxonomic profiling revealed the association of microbial dysbiosis with extreme sickness in both humans and broiler chickens. The dominance of phylum Proteobacteria in both the species ascertains their altered gut microbiota. Both human and broiler chickens microbial communities were found to be genetically related indicating horizontal transfer of microbes between the two species.

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Next-generation sequencing of BRCA1 and BRCA2 in breast cancer patients and control subjects

Molecular and Clinical Oncology ◽

10.3892/mco.2014.251 ◽

2014 ◽

Vol 2 (3) ◽

pp. 435-439 ◽

Cited By ~ 6

Author(s):

LUBOMIR BALABANSKI ◽

GEORGI ANTOV ◽

IVANKA DIMOVA ◽

SAMUIL IVANOV ◽

MARIA NACHEVA ◽

...

Keyword(s):

Breast Cancer ◽

Next Generation Sequencing ◽

Cancer Patients ◽

Next Generation ◽

Breast Cancer Patients ◽

Brca1 And Brca2 ◽

Control Subjects ◽

And Control ◽

Generation Sequencing

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Comparison of different hypervariable regions of 16S rRNA for taxonomic profiling of vaginal microbiota using next-generation sequencing

Archives of Microbiology ◽

10.1007/s00203-020-02114-4 ◽

2020 ◽

Author(s):

Auttawit Sirichoat ◽

Nipaporn Sankuntaw ◽

Chulapan Engchanil ◽

Pranom Buppasiri ◽

Kiatichai Faksri ◽

...

Keyword(s):

Next Generation Sequencing ◽

16S Rrna ◽

Vaginal Microbiota ◽

Next Generation ◽

Taxonomic Profiling ◽

Hypervariable Regions ◽

Generation Sequencing

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Influence of Next-Generation Sequencing and Storage Conditions on miRNA Patterns Generated from PAXgene Blood

Analytical Chemistry ◽

10.1021/acs.analchem.5b02043 ◽

2015 ◽

Vol 87 (17) ◽

pp. 8910-8916 ◽

Cited By ~ 19

Author(s):

Christina Backes ◽

Petra Leidinger ◽

Gabriela Altmann ◽

Maximilian Wuerstle ◽

Benjamin Meder ◽

...

Keyword(s):

Next Generation Sequencing ◽

Storage Conditions ◽

Next Generation ◽

And Storage ◽

Generation Sequencing

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Genomic characterization of fecal microbial communities in severely sick humans and broiler chickens using next generation sequencing

10.21203/rs.2.21973/v1 ◽

2020 ◽

Author(s):

Ome Kalsoom Afridi ◽

Johar Ali ◽

Jeong Ho Chang

Keyword(s):

Next Generation Sequencing ◽

Microbial Communities ◽

Broiler Chickens ◽

Human Subjects ◽

Fecal Microbiota ◽

Next Generation ◽

Microbial Association ◽

Taxonomic Profiling ◽

Microbial Dysbiosis ◽

Generation Sequencing

Abstract BackgroundMicrobiota plays an important role in food safety and its alteration poses a serious threat to humans. Comparative microbiome profiling using next-generation sequencing (NGS) enabled the understanding of microbial diversity and similarity between different species. In this study, we used NGS to profile the fecal microbiota of sick human and broiler chickens. A total of 26 fecal samples were collected from severely sick human subjects (n= 13) and broiler chickens (n=13) with similar symptoms.ResultsThe total number of microbial species detected in broiler chickens fecal microbiota was higher than that of humans. Phylum Proteobacteria was the most abundant in both human and broiler chickens fecal microbiota while Tenericutes was found to be least abundant in both species. Phylum Actinobacteria was found only in the human fecal microbiota. In both humans and broiler chickens, E.coli was found to be phylogenetically related suggesting a microbial association between both species.ConclusionNGS based taxonomic profiling revealed the association of microbial dysbiosis with extreme sickness in both humans and broiler chickens. The dominance of phylum Proteobacteria in both the species ascertains their altered gut microbiota. Both human and broiler chickens microbial communities were found to be genetically related indicating horizontal transfer of microbes between the two species.

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A next-generation sequencing study on mechanisms by which restraint and social instability stresses of male mice alter offspring anxiety-like behavior

Scientific Reports ◽

10.1038/s41598-021-87060-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Qiao-Qiao Kong ◽

Xiao-Dan Tian ◽

Jia Wang ◽

Hong-Jie Yuan ◽

Shu-Fen Ning ◽

...

Keyword(s):

Dna Methylation ◽

Next Generation Sequencing ◽

Female Offspring ◽

Next Generation ◽

Transgenerational Transmission ◽

Social Instability ◽

Sperm Dna ◽

And Control ◽

Generation Sequencing ◽

Sperm Dna Methylation

AbstractPathophysiological mechanisms for depression/anxiety are largely unknown. Evidence for transgenerational transmission of acquired epigenetic marks remains limited. We bred unstressed (US) female mice with adolescently restraint-stressed (RS), social instability-stressed (SI) or US males to produce RS, SI and control F1 offspring, respectively. Compared to controls, while paternal RS decreased anxiety-like behavior (ALB) in both female and male offspring, paternal SI increased ALB only in female offspring. Next-generation sequencing and bioinformatics using RS and SI female offspring identified 5 candidate anxiety-transmitting (CAT) genes; each showed a consistent pattern of DNA methylation from F0 spermatozoa through F1 blastocysts to fetal and adult hippocampi. Further analyses validated 4 CAT genes, demonstrated that paternal SI caused ALB differences between male and female offspring through modifying the CAT genes, and indicated a strong correlation between inflammation and ALB pathogenesis and an important function for intronic DNA methylation in regulating ALB-related genes. In conclusion, this study identified important CAT genes and suggested the possibility that stresses on males might alter offspring’s ALB by modifying sperm DNA methylation.

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